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112 results for “Time trees”
Data from: Multidimensional environmental influences on timing of breeding in a tree swallow population facing climate change
Most phenological traits are extremely sensitive to current climate change and advances in the timing of important life-history events have been observed in many species. In birds, phenotypic plasticity in response to temperature is thought to be the main mechanism underlying yearly adjustment in the timing of breeding. However, other factors could be important and interact to affect the levels of plastic responses between and/or within-individuals. Here we use long-term individual-based data on Tree swallow (Tachycineta bicolor) to identify the spatial and environmental drivers affecting plasticity in laying date and to assess their importance at both population and individual levels. We found that laying date has advanced by 4.2 days over 10 years, and that it was mainly influenced by latitude and an interaction between spring temperature and breeder density. Analyses of individual plasticity showed that increases in temperature, but not in breeder density, resulted in within-individual advances in laying date. Our results suggest that females can adjust their laying date as a function of temperature, but that this adjustment will be partly constrained in habitats with lower breeder densities. Such potential constraint is especially worrying for the broad array of species already declining as a result of climate change.
Data from: Measuring stratigraphic congruence across trees, higher taxa, and time
The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index, the modified Manhattan stratigraphic measure, and the gap excess ratio (plus its derivatives; the topological gap excess ratio and the modified gap excess ratio). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence dates, center of gravity of first occurrence dates, the variability of first occurrence dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published vertebrate and invertebrate cladograms spanning the entire Phanerozoic, and for these data we also modelled the effects of mean age of first occurrences (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of first occurrence dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified gap excess ratio was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence – however measured – also varied throughout the Phanerozoic, reflecting the taxonomic composition of our sample. Notably, periods containing a high proportion of arthropods had poorer congruence overall than those with higher proportions of tetrapods.
Data from: A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity
The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135–130 million yr ago (Ma); Pentapetalae is 126–121 Ma; and Rosidae (123–115 Ma) preceded Asteridae (119–110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 in The phylogenetIc posItIon and taxonomIc status of the RaInbow Tree Snake Gonyophis margaritatus (Peters, 1871) (Squamata: ColubrIdae)
FIGURE 1. Time-calibrated phylogeny including 101 taxa built using program BEAST v1.7.5 (Drummond et al. 2012) with node support values representing posterior probability (left) and bootstrap support (right) from inferred Maximum Likelihood tree. Dashes for bootstrap values indicate low support or not supported by ML tree. Family Colubridae and subfamily Colubrinea are highlighted by red arrows. Taxa in genera Gonyosoma, Rhadinophis, Gonyophis, and Rhynchophis are highlighted in the red square on the tree.
FIGURE 8. Ultrametric time tree obtained from Analysis 5 in Flightless Notaris (Coleoptera: Curculionidae: Brachycerinae: Erirhinini) in Southwest China: monophyly, mtDNA phylogeography and evolution of habitat associations
FIGURE 8. Ultrametric time tree obtained from Analysis 5 by using BEAST software to date evolutionary events of the Notaris + Tournotaris clade. Numbers at nodes and on the scale below are million years before present. Node bars represent 95% confidence interval of the age estimate. Alternating snowflake and sun symbols denote Pleistocene climatic fluctuations.
Figure 1. A, Bayesian time tree for Hemiphyllodactylus with 95 in Repeated evolution of sympatric, palaeoendemic species in closely related, co-distributed lineages of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) across a sky-island archipelago in Peninsular Malaysia
Figure 1. A, Bayesian time tree for Hemiphyllodactylus with 95% highest posterior density (95% HPD) intervals for major nodes represented by purple bars. Black circles at nodes are posterior probabilities ≥ 0.95; grey circles at nodes are posterior probabilities <0.95. B, Bayesian time tree for the Hemiphyllodactylus harterti group. C, Distribution of the H. harterti group in Peninsular Malaysia.
Figure 2. The maximum likelihood tree inferred from 14 594 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 2. The maximum likelihood tree inferred from 14 594 nucleotide sites of 60 Cypriniformes and six outgroups (lnL = -203 966.535). Numbers at each branch indicate the resampling the estimated log likelihood (RELL) local bootstrap probabilities. Asterisks indicate 100% local bootstrap support. Two major clades of Cyprinidae (A and B) correspond with those presented in Cavender & Coburn (1992).
Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)
<div> <div> <div> <p>Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (<em>Ibidorhyncha</em>), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.</p> </div> </div> </div>
FIGURE 1. Bayesian time-tree for 32 in A review of all Recent species in the genus Novocrania (Craniata, Brachiopoda)
FIGURE 1. Bayesian time-tree for 32 craniids, specimen details and clade names as in Cohen, Kaulfuss et al. (2014), based on the alignment shown in Supplementary file 1. The root node height (relative age) is defined as 1.0 and other mean node heights (relative ages) are shown in proportion to the root node. The gray bars across nodes show the 95% highest posterior density ranges, roughly equivalent to 95% confidence intervals. Note that other analyses may place the root node elsewhere in the craniid radiation.
Data for the study "'Look at the Trees': A Verbal Nudge to Reduce Screen Time When Learning Biodiversity with Augmented Reality"
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Data from: Thermal differences between juveniles and adults increased over time in European forest trees
<p><span>Woody species' requirements and environmental sensitivity change from seedlings to adults, a process referred to as ontogenetic shift. Such shifts can be increased by climate change. To assess the changes in the difference of temperature experienced by seedlings and adults in the context of climate change, it is essential to have reliable climatic data over long periods that capture the thermal conditions experienced by the individuals throughout their life cycle. </span></p> <p><span>Here we used a unique cross-European database of 2195 pairs of resurveyed forest plots with a mean intercensus time interval of 37 years. We inferred macroclimatic temperature (free-air conditions above tree canopies – representative of the conditions experienced by adult trees) and microclimatic temperature (representative of the juvenile stage at the forest floor, inferred from the relationship between canopy cover, distance to the coast, and below-canopy temperature) at both surveys. We then address the long-term, large-scale, and multitaxa dynamics of the difference between the temperatures experienced by adults and juveniles of 25 temperate tree species.</span></p> <p><span>We found significant, but species-specific, variations in the perceived temperature (calculated from presence/absence data) between life stages during both surveys. Additionally, the difference of the temperature experienced by the adult versus juveniles significantly increased between surveys for eight of 25 species. We found evidence of a relationship between the difference of temperature experienced by juveniles and adults over time and one key functional trait (i.e. leaf area). Together, these results suggest that the temperatures experienced by adults vs juveniles became more decoupled over time for a subset of species, probably due to the combination of climate change and a recorded increase of canopy cover between the surveys resulting in higher rates of macroclimate than microclimate warming. </span></p> <p><span>Synthesis: We document warming and canopy-cover induced changes in the difference of the temperature experienced by juveniles and adults. These findings have implications for forest management adaptation to climate change such as the promotion of tree regeneration by creating suitable species-specific microclimatic conditions. Such adaptive management will help to mitigate the macroclimate changes in the understory layer.</span></p>
Figure 2 in Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)
Figure 2. Phylogenetic tree showing the reconstructed ancestral geographical distributions for extant and ancestral drosophilids estimated by the maximum-likelihood algorithm. Extant geographical distributions were retrieved from the Drosophila Stock Center or from the ZipcodeZoo database. See Table S2 for geographical distributions.
Figure 1 in Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae)
Figure 1. Timescale for drosophilids based on a maximum-likelihood (ML) analysis using a concatenated alignment (9917 bp) of six protein-coding nuclear genes. Several monophyletic branches have been collapsed, indicating that all taxa within that taxonomic rank form a cluster. Support values above branches are bootstrap proportions performed on the ML tree; values less than 50 are not shown.
FIGURE 1. Strict consensus tree from a in Biogeography and divergence time estimation of the relict Cape dragonfly genus Syncordulia: global significance and implications for conservation
FIGURE 1. Strict consensus tree from a PAUP parsimony heuristic search; 10,000 addition sequence replicates; bootstrap support shown above branches
FIGURE 2. Consensus tree from a in Biogeography and divergence time estimation of the relict Cape dragonfly genus Syncordulia: global significance and implications for conservation
FIGURE 2. Consensus tree from a PHASE analysis; 10 million generations. Posterior probabilities shown above branches
Attack time analysis in dynamic attack trees via integer linear programming
<p>Code and data corresponding to the paper "Attack time analysis in dynamic attack trees via integer linear programming"</p>
Selection in space and time: individual tree growth is adapted to tropical forest gap dynamics
<p>In the present study, we assessed genotypic diversity within closely-related sympatric tree species belonging to the widespread tropical tree species complex <em>Symphonia globulifera</em>. We addressed the fine-scale spatial and temporal genetic adaptations of individuals through differential growth strategies in response to forest gap dynamics. We finally compared the breadth of successional niches encountered by <em>Symphonia</em> species to other locally abundant species. Combining tree diameter censuses, indirect measures of light environment of the recent past and present, and single nucleotide polymorphisms (SNPs), we used population genomics, environmental association analyses, genome wide association and growth modelling to address the following questions:</p> <ul> <li>Are individual genotypes structured by the mosaic of light and competition environments resulting from forest gap dynamics?</li> <li>Is the growth of individuals determined by genotypes?</li> <li>Is there an association between genotypic adaptations to gap dynamics and to growth?</li> <li>How are genotypic adaptations to gap dynamics and to growth structured in time, i.e., across life stages?</li> <li>Are breadths of successional niches for <em>Symphonia</em> species wider than those of other locally abundant species?</li> </ul> <p>Find the analyses here : https://sylvainschmitt.github.io/GOING/introduction.html</p>
Data from: Phylogenetic relationships within the lizard clade Xantusiidae: using trees and divergence times to address evolutionary questions at multiple levels
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Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays
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Data from: Tree ring δ15N as validation of space-for-time substitution in disturbance studies of forest nitrogen status
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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